Package: CytoSimplex 0.2.0

Yichen Wang

CytoSimplex: Simplex Visualization of Cell Fate Similarity in Single-Cell Data

Create simplex plots to visualize the similarity between single-cells and selected clusters in a 1-/2-/3-simplex space. Velocity information can be added as an additional layer. See Liu J, Wang Y et al (2023) <doi:10.1093/bioinformatics/btaf119> for more details.

Authors:Yichen Wang [aut, cre], Jialin Liu [aut], Joshua Welch [cph]

CytoSimplex_0.2.0.tar.gz
CytoSimplex_0.2.0.zip(r-4.7)CytoSimplex_0.2.0.zip(r-4.6)CytoSimplex_0.2.0.zip(r-4.5)
CytoSimplex_0.2.0.tgz(r-4.6-x86_64)CytoSimplex_0.2.0.tgz(r-4.6-arm64)CytoSimplex_0.2.0.tgz(r-4.5-x86_64)CytoSimplex_0.2.0.tgz(r-4.5-arm64)
CytoSimplex_0.2.0.tar.gz(r-4.7-arm64)CytoSimplex_0.2.0.tar.gz(r-4.7-x86_64)CytoSimplex_0.2.0.tar.gz(r-4.6-arm64)CytoSimplex_0.2.0.tar.gz(r-4.6-x86_64)
CytoSimplex_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CytoSimplex/json (API)

# Install 'CytoSimplex' in R:

install.packages('CytoSimplex', repos = c('https://welch-lab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/welch-lab/cytosimplex/issues

Pkgdown/docs site:https://welch-lab.github.io

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

rnaCluster - Major cell type annotation of the example mouse bone marrow data
rnaRaw - Mouse bone marrow scRNAseq example data
rnaVelo - Velocity graph of the example mouse bone marrow data

On CRAN:

openblas cpp

4.78 score 6 stars 5 scripts 577 downloads 10 exports 71 dependencies

Last updated from:d8a252f08a. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	255
linux-devel-x86_64	OK	275
source / vignettes	OK	362
linux-release-arm64	OK	244
linux-release-x86_64	OK	273
macos-release-arm64	OK	247
macos-release-x86_64	OK	419
macos-oldrel-arm64	OK	207
macos-oldrel-x86_64	OK	364
windows-devel	OK	207
windows-release	OK	254
windows-oldrel	OK	210
wasm-release	OK	192

Exports:colNormalize plotBinary plotQuaternary plotTernary readH5ADObsNames readH5ADObsVar readH5ADUnsSpMat readVelocytoLoom selectTopFeatures writeQuaternaryGIF

Dependencies:askpass base64enc bslib cachem cli cpp11 crosstalk curl data.table digest dplyr evaluate farver fastmap fontawesome fs generics ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr Matrix memoise mime misc3d openssl otel pillar pkgconfig plot3D plotly promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo rlang rmarkdown S7 sass scales stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridis viridisLite withr xfun yaml

Simplex Visualization of Cell Fate Similarity in Single-Cell Data

Rendered fromCytoSimplex.Rmdusingknitr::rmarkdown

Last update: 2025-04-23
Started: 2023-09-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Normalize each column of the input matrix by the column sum	colNormalize colNormalize.default colNormalize.dgCMatrix colNormalize.Seurat colNormalize.SingleCellExperiment
Create binary plots	plotBinary plotBinary.default plotBinary.Seurat plotBinary.simMat plotBinary.SingleCellExperiment
Create quaternary simplex plots	plotQuaternary plotQuaternary.default
Craete quaternary simplex plot with Seurat object	plotQuaternary.Seurat
Create quaternary simplex plot with pre-calculated similarity matrix	plotQuaternary.simMat
Create quaternary simplex plot with SingleCellExperiment object	plotQuaternary.SingleCellExperiment
Create ternary simplex plots	plotTernary plotTernary.default
Create ternary simplex plot with Seurat objects	plotTernary.Seurat
Create quaternary simplex plot with pre-calculated similarity matrix	plotTernary.simMat
Create ternary simplex plot with SingleCellExperiment objects	plotTernary.SingleCellExperiment
Show plist object produced with plot3D package	print.quatPlot
Extract `adata.obs_names` from an H5AD file	readH5ADObsNames
Extract a variable from adata.obs stored in an H5AD file	readH5ADObsVar
Extract a sparse matrix from adata.uns stored in an H5AD file	readH5ADUnsSpMat
Extract the raw counts from a LOOM file	readVelocytoLoom
Major cell type annotation of the example mouse bone marrow data	rnaCluster
Mouse bone marrow scRNAseq example data	rnaRaw
Velocity graph of the example mouse bone marrow data	rnaVelo
Pick top differentially presented features for similarity calculation	selectTopFeatures selectTopFeatures.default selectTopFeatures.Seurat selectTopFeatures.SingleCellExperiment
Create GIF image for dynamic rotating view of 3D quaternary simplex plot	writeQuaternaryGIF